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    190 repositories

    • tfmodisco

      Public
      TF MOtif Discovery from Importance SCOres
      Python
      •
      MIT License
      •32•166•3•2•Updated Feb 20, 2026Feb 20, 2026

    • histobpnet

      Public
      Sequence to histone models
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•0•0•0•Updated Feb 18, 2026Feb 18, 2026

    • klf_smf

      Public
      Paper on KLF SMF with the Will Greenleaf lab
      Jupyter Notebook
      •0•0•0•0•Updated Feb 14, 2026Feb 14, 2026

    • regulatory_lm

      Public
      The official repository for the ARSENAL model
      Jupyter Notebook
      •0•10•0•0•Updated Feb 13, 2026Feb 13, 2026

    • DART-Eval

      Public
      Jupyter Notebook
      •5•44•3•0•Updated Feb 11, 2026Feb 11, 2026

    • igvf_pseudobulking_pipeline

      Public
      Code for assisting with pseudobulking IGVF single cell data.
      Python
      •1•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • chrombpnet

      Public
      Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
      Jupyter Notebook
      •
      MIT License
      •55•210•21•3•Updated Feb 2, 2026Feb 2, 2026

    • varscore

      Public
      Core functions for variant scoring
      Python
      •0•1•5•0•Updated Feb 1, 2026Feb 1, 2026

    • MotifCompendium

      Public
      HTML
      •0•7•0•0•Updated Jan 25, 2026Jan 25, 2026

    • tangermeme

      Public
      Biological sequence analysis for the modern age.
      Python
      •
      MIT License
      •27•0•0•0•Updated Jan 16, 2026Jan 16, 2026

    • chrombpnet-pytorch

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •7•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • gp_mouse

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 28, 2025Nov 28, 2025

    • Fi-NeMo

      Public
      Identifying transcription factor binding sites from neural network contribution scores
      Python
      •
      MIT License
      •0•17•0•2•Updated Nov 8, 2025Nov 8, 2025

    • shap

      Public
      A unified approach to explain the output of any machine learning model.
      Jupyter Notebook
      •
      MIT License
      •3.5k•10•0•1•Updated Oct 23, 2025Oct 23, 2025

    • IGVF_helpers

      Public
      Scripts to help with IGVF single cell processing
      Python
      •0•0•0•0•Updated Oct 21, 2025Oct 21, 2025

    • scATAC-reprog

      Public
      Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibro…
      Jupyter Notebook
      •
      MIT License
      •2•12•1•0•Updated Oct 16, 2025Oct 16, 2025

    • bpnet

      Public
      Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them
      Python
      •
      MIT License
      •38•175•0•0•Updated Oct 10, 2025Oct 10, 2025

    • bpnet-refactor

      Public
      Python
      •
      MIT License
      •4•8•5•1•Updated Sep 22, 2025Sep 22, 2025

    • ProCapNet

      Public
      Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
      Jupyter Notebook
      •
      MIT License
      •3•19•0•0•Updated Aug 28, 2025Aug 28, 2025

    • e2g-frontend

      Public
      TypeScript
      •
      Apache License 2.0
      •0•2•0•0•Updated Aug 20, 2025Aug 20, 2025

    • variant-scorer

      Public
      A framework to score and analyze variant effects genome-wide using ChromBPNet models
      Python
      •
      MIT License
      •5•16•2•0•Updated Aug 1, 2025Aug 1, 2025

    • kundajelab.github.io

      Public
      HTML
      •
      MIT License
      •0•0•5•0•Updated Jul 26, 2025Jul 26, 2025

    • hubmaker

      Public
      A utility to programmatically make trackhub JSON files for a genome browser.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 14, 2025Jul 14, 2025

    • v2f-frontend

      Public archive
      JavaScript
      •
      Apache License 2.0
      •0•1•0•0•Updated Jun 11, 2025Jun 11, 2025

    • archive

      Public
      HTML
      •0•0•0•0•Updated May 5, 2025May 5, 2025

    • bam2bw

      Public
      A command-line tool for reading SAM/BAM files and converted them directly to bigwig files.
      Python
      •
      MIT License
      •3•0•0•0•Updated May 1, 2025May 1, 2025

    • ImmuneCLIP

      Public
      CLIP-based model for aligning epitopes to immune receptors
      Python
      •
      MIT License
      •1•12•0•0•Updated Apr 30, 2025Apr 30, 2025

    • variant-scorer-procapnet

      Public
      A framework to score and analyze variant effects genome-wide using ProCapNet models
      Python
      •
      MIT License
      •5•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • neuro-variants

      Public
      This repository contains all scripts for the manuscript "Mapping the regulatory effects of common and rare non-coding variants across cellular and developmental…
      Jupyter Notebook
      •0•3•0•0•Updated Feb 19, 2025Feb 19, 2025

    • kundajelab_old.github.io

      Public
      Official Kundaje Lab Blog
      HTML
      •0•0•0•2•Updated Jan 31, 2025Jan 31, 2025